Chuck versus the Bunker
by timewalker05
Summary: A stupid little one-shot. AU following Chuck's extraction in Chuck versus the Marlin. What if Lizzie didn't show and Chuck was sent to the bunker by Beckman and Graham?


I needed a break from "Chuck versus the Decision" and I didn't want to start back on "Buy More Bomber" until I could devote time to really knocking it out, so I did another one shot. I promise, I'll get back to Decision now and then I'll make a concerted effort on Bomber, which has been languishing.

Credit **Poa** if you like this. She made some great suggestions (and proofread it as well). If you don't like it, that's all me.

CHUCKVERSUS THE BUNKER

Longshore keyed his radio. "The package is ready for extraction. Send in the chopper."

Longshore dragged a handcuffed Chuck Bartowski up to the building roof. He glanced behind them, then up at the sky, looking for the helicopter that would whisk 'the package' to an undisclosed location. This was Longshore's expertise. He had handled dozens of extractions of important assets from locations a lot riskier than downtown Los Angeles.

"Longshore!" Longshore spun around and put his hand on his gun. Agent Sarah Walker came running up the stairs to the rooftop helipad, her blonde hair streaming in the wind.

"Is there a problem Agent Walker?" Longshore demanded.

Chuck held up his hands as best he could with the cuffs on. He looked pleadingly at Sarah. "Sarah, thank God you're here. Listen, I don't want to go yet. I... I ca-…"

"Agent Casey is tracking the Fulcrum mole and he should have her in custody soon," Sarah said. "So we can hold off on the Chuck transfer for the time being." There was a subtle note of pleading in her voice.

Longshore looked at her with the hard look of a trained agent. "If there was a change in the operation I would have been contacted. I have my orders." Chuck looked at him, horrified.

"We don't have to do this. This is a judgment call," Sarah said, holding her hands out by her sides. "Okay, we can just hold Chuck here until we know for sure."

Longshore's tone was angry. He couldn't believe an agent, one of the supposed 'good guys' was disrupting his operation like this. "His cover was blown. He's gone." He grabbed Chuck by the arm.

"No. I will take full responsibility," Sarah said. "Chuck is my asset. He's my guy. Just give us more time, please."

Chuck looked at Sarah nervously, trying to swallow the lump in his throat that would not go away. "I'd appreciate it," he begged Longshore. "I really would." Longshore looked from Sarah, to Chuck and back to Sarah.

"Please don't do this," Sarah asked again. She reached behind her, hand on the gun tucked into the waistband of her pants. She wasn't exactly sure what she would do, but she couldn't let Chuck be taken away. Not like this.

"Okay. You've got one minute," Longshore said. He held up a finger to emphasize the point. "One minute."

Sarah sidled over to Chuck, circling to keep her eyes on Longshore. And, incidentally, not to expose the gun in her waistband. Sarah looked up at Chuck. He had never looked so desperate. "I'm not ready, Sarah. I'm not ready to disappear."

"No," Sarah nodded. "I know. I know."

"I need you to talk to Ellie. And to Morgan and my friends." Sarah's heart was breaking. Nothing was more important to Chuck than family. And here he was about to be taken away, never to see them again. Tears began to well up in her eyes.

"And, and, and tell them," Chuck continued. "I don't know. Look, if I'm supposed to be dead then just say something that will make it okay. That will make them feel all right. Just make sure they know how much I love them. You can do that, right?"

Sarah's eyes were brimming with tears now. She gave a small shake of her head. "Of course you can," Chuck said. You're Sarah. You can do anything. And hey! There's a silver lining to this too, you know?" Chuck gave a short, sad laugh. "Cause we're not working together anymore. Which means we can go on a date? You can come by my cell, and we can hang out, and you can tell me who the president is." Sarah laughed. Leave it to Chuck to try to make her laugh even at a time like this.

"And maybe, uh…" Chuck reached out to Sarah and she put her hands in his. "Maybe we can see how we really feel." Chuck was choked up now and Sarah was on the verge of breaking down.

Longshore looked up. The helicopter was approaching. "Time's up."

Chuck looked over at Longshore, than back at Sarah. "Goodbye, Sarah." A single tear escaped from Sarah's eye and fell down her cheek. Chuck let go of her hands and turned quickly, as if he couldn't bear to look at her any more.

"Chuck!" Chuck stopped and turned around to look back at Sarah. "Save you later."

Chuck almost smiled and gave Sarah a single nod. Then he turned back to Longshore. Sarah watched him approach the agent and was torn about what to do. A moment ago, she had been ready to pull her gun to keep Longshore from taking Chuck. But that would only mean that the two of them would have to run and Chuck still would never see his family again.

The whump, whump, whump of rotors filled the air and Sarah had to run to the side of the roof, away from the center of the helipad. It was too late now. The helicopter was here to take Chuck away.

Longshore moved Chuck to the side and they both squinted into the blast from the rotor blades. The helicopter hovered for a moment as the pilot surveyed the scene on the roof, then touched down. A man in the back opened the side door. "Longshore?" he called. "Extraction code All Star."

Longshore nodded and motioned Chuck to duck as they hurried to the helicopter. The man in the back pulled Chuck in and Longshore climbed in after him. Then the door slammed shut and the whine of the rotor blades grew louder again as the chopper slowly lifted from the roof. Sarah watched it go until it was a tiny speck of light. "Goodbye, Chuck," she said softly, the tears streaming freely down her face now.

*************************

The 'bunker', Chuck had discovered, was really a rather plush underground facility. His suite of rooms included a living room, dining room, bedroom, bathroom and even a small kitchen. The living room had a huge plasma T.V. with an Xbox 360, a Playstation 3 and a Wii. His 'resident assistant' – jailer was such a harsh term – even brought him all the latest videogames and gaming magazines. Once in a great while, he even talked one of his handlers into playing a game with him, although they all sucked at it. But Chuck was a nice guy and they felt sorry for him, so they dutifully took turns being the sacrificial lamb that got pummeled by the resident nerd.

He had more HD channels than he could possibly watch, with all the premium channels, and even unlimited pay per view. He even had a computer, although it was a stand-alone and had no network or Internet access. The food was good; he had put on almost twenty pounds since he had entered the bunker.

Once a month, he was taken 'outside' to secure locations. That meant he could go shopping (after hours when there were no other customers in the store) or go for a walk in the park ('the park' being a heavily guarded green space in the middle of a military base.)

All in all, Morgan would have considered it heaven (other than the fact that he wouldn't have been able do any of his gaming on-line and he wouldn't have had access to his on-line porn.)

He had been in the bunker twenty-two months now. Every three months, Sarah Walker stopped by for a visit. At first, Chuck had enjoyed the visits. Now he dreaded them. After all, he only got to see her for a few hours and then under close supervision. Sarah couldn't even tell him what she had been doing. So the visits had grown to be an agony for him. It was like showing a diabetic pictures of desserts and telling him he could never taste them. He considered asking her to stop coming, but he couldn't bring himself to do it.

He had a routine that only varied on those days when he went 'outside' or Sarah visited. He would be awakened every morning at eight – at least they let him sleep in. Then they would take him to the facilities workout room and force him to exercise. After a shower and breakfast, they would sit him down on the couch in front of his big plasma television and show him various intel to see if he flashed on anything. This would go on until lunch. The afternoons and evenings were his own to do as he pleased. Once in a while, they would come in at any hour of the day or night (although he couldn't really tell the difference) with some special intel for him to look at.

He had tried to get them to train him as an agent, reasoning that if he knew how to defend himself maybe they would let him back out on missions again. But the word had come down from General Beckman. Training as an agent was out of the question. It was too dangerous and he was too valuable to risk in the field. Chuck had heard rumors that the attempt to build a new Intersect had met with disaster, so he was the only available Intersect for the foreseeable future.

So Chuck studied (finishing his bachelor's degree and getting a correspondence Master's degree in Electrical Engineering) and becoming conversant in French, German and Spanish. Now he was learning Russian. He figured that by the time he got out (if he ever got out); he would have several degrees and speak a host of languages.

Then came 'The Day.' It had started like any other day. They woke him precisely at eight o'clock (funny, he didn't even know what time zone that was) and marched him down to the gym for his workout. Then a shower and breakfast. After breakfast, he sat down on his couch waiting for his morning 'flash session.' But nothing happened. He waited and waited. Finally he got bored and Put Madden 2011 in his Xbox and was getting ready to start a game when the door to his room opened.

"Come with me," the handler he knew only as 'Frank' said.

"Where are we going?" Chuck asked.

"Out," was the only reply.

Chuck shrugged and followed Frank out. They went down the hall and got in the elevator for the long ride to the surface.

Frank signed them out with the guard at the surface. Then they walked out the big steel doors to the outside. Chuck blinked in the bright sunlight. He hadn't seen the sun in nearly two weeks. He squinted and shaded his eyes. He felt Frank put something in his hand. He blinked and his eyes watered as he looked at what it was – a pair of sunglasses. Chuck slipped them on. The light still hurt, but this was marginally better.

Frank too his arm and motioned him forward toward a waiting long, black limousine. He opened the door and guided Chuck inside. With its dark interior and tinted windows, Chuck's eyes no longer hurt. They drove to a nearby airstrip. The limo pulled into a hanger where a government G-4 was waiting. They pulled up next to the plane and Frank got out, then held the door for Chuck.

The ramp of the G-4 was lowered and a pair of agents flanked the ramp. Chuck recognized them immediately: Casey and Walker. As soon as she saw him, Sarah abandoned all propriety and hurried over to give Chuck a hug.

"Hello, Chuck."

"Sarah. What's going on?" Chuck asked. "Where are you taking me?"

"Later," Sarah whispered.

"Hello, Casey," Chuck said.

"Bartowski," Casey said with a slight nod of the head.

"We have to get going," Sarah said. "We're going to be late." She took Chuck's hand and led him up the ramp and into the plane. Casey followed behind and then pulled the ramp up behind them.

Sarah motioned Chuck to a seat and then took the one facing him. "Better strap in," she warned him. Casey took a seat further back and Chuck heard him grumble something about letting someone else fly him around.

"What's going on?" Chuck asked. But just then the engines fired up. Moments later, the plane started to move.

The plane pulled out of the hanger and turned onto the taxiway and then directly onto the runway. There was only a slight pause while the engines were run up, and then they were rolling down the runway and airborne.

"So, I'm going to ask again. What's going on? Did they build the new Intersect? Are they setting me free?"

Sarah shot a glance at Casey. "I'm not supposed to say anything," Sarah said.

"Come on, Sarah. I've been in that damned bunker for twenty-two months. Now, all of a sudden, I'm pulled out, whisked away to the airport where you and Casey are waiting, stuffed in a plane and now I'm off to parts unknown."

Sarah laid her hand on Chuck's. "It's going to be okay," Sarah said. "Don't worry. This is a good thing."

"Then why can't you tell me?"

"Orders, Bartowski," Casey bellowed from the back of the plane. "So just shut up about it."

Chuck turned and glared at Casey. "Like hell, Casey. And thanks for stopping by to see me while I was away. That was nice of you." He continued to stare at Casey until finally Casey averted his gaze and looked down at the floor.

"Hell, Walker," Casey said. "Tell him. What the hell can it hurt now? The cat's out of the bag."

Chuck turned back to Sarah to see her smiling at him. "Yes, Chuck, you're being set free. We're on our way to see Beckman now."

"So what happened?" Chuck asked. "Did they finally get the new Intersect up and running?"

"It's a long story," Sarah said.

"So how long is the flight?" Chuck asked.

Sarah grinned. "It's all Ellie's fault." Chuck frowned and looked at her, confused.

"That night on the rooftop, after Longshore took you away, you remember?"

"How could I forget?" Chuck asked, a note of disgust in his voice.

"After you left, I was supposed to go immediately to my hotel, pack up my things, and return immediately to D.C. for reassignment. You see, if your cover had been blown, then Casey's and mine had been, too."

"I guess that makes sense," Chuck said.

"But after what you said on the roof, I couldn't just leave. Not without saying something to Ellie. So I went over to her apartment. When I knocked on the door, Ellie answered. She told me that you weren't there. I took her out in front of the complex, away from the listening devices…" There was a grunt from the back from Casey. Unfortunately, it had been too long. Chuck was a little rusty translating Casey grunts.

"Once we were outside I told her you were gone. I told her that you had to leave suddenly but that you were all right. I couldn't tell her where you had gone or why. Just that you loved her very much and it was not your fault, but you could never see her again; for her own safety as well as yours. For your sake, she couldn't tell anyone what I had just told her. She just had to tell everyone that you had disappeared. She yelled at me, she pleaded with me, but I couldn't tell her anything. Finally I just had to walk away."

The plane hit a bit of turbulence and dropped suddenly. Chuck gripped the armrests of his chair, his knuckles turning white. This was only his second trip on a small plane – the first had been the trip to the bunker. Come to think of it, that made it his second airplane trip ever. Sarah reached over and placed her hand on his and smiled. "Are you okay?"

The ride smoothed out and Chuck nodded. "I'm not used to planes," he said.

Sarah patted his hand and continued. "Ellie couldn't let it go. She went to the police. She hired a private investigator. The CIA blocked her at every turn. Finally, she had hit a dead end."

"Didn't think she'd ever give up," Casey grumbled. "She was like a bloodhound on a scent. Pretty decent investigative skills, too." Chuck glanced at him. Praise from Casey? That was like snow in July. In Hawaii.

Sarah continued her story. "Ellie's wedding to Devon was delayed, but they finally got married, like I told you on one of my visits. I actually attended, though no one knew I was there. It was a happy day but you could tell Ellie was sad not to have any family there."

"They bought a house and were packing up their things to move. Up until that point, she had kept your room exactly as you left it. But in packing up your things, she came across something that told her what had really happened."

His room. What had she found? Then it dawned on him. "She found the shoebox." Whenever Chuck forgot to turn his i.d.'s back in, Chuck had stored his CIA issue fake identification in a shoebox under his bed.

Casey snorted from the back. "No, Chuck," Sarah said. "Not the shoebox. When you were taken away, Casey searched your room and found the shoebox."

"Pretty stupid leaving that in a shoebox under the bed, Bartowski," Casey growled.

"Sorry," Chuck said, glaring at Casey. "I didn't get much training in how to be a spy." His tone was bitter and once again it was Casey who looked away.

"We don't know what it was," Sarah said. "But suddenly Ellie knew about the Intersect, me, Casey, Graham, Beckman, Bryce, Fleming, Lazlo, even Ilsa."

"Oh my God," Chuck whispered. "Tron."

"What?" Sarah asked.

"I wasn't content to be a mere pawn," Chuck said. "I was trying to figure out the Intersect myself. I was keeping a chart with all of the various data and connections to help me figure it out."

"Impossible," Casey said. "I would have found it."

Chuck ignored him. "Ellie must have found it."

"Where was it?" Sarah asked.

"On the back of my Tron poster," Chuck said.

There was a disgusted sound from behind him. "Damn," Casey spat. "Leave it to a nerd."

"Well," Sarah said. "Now Ellie had something to go on. Once she figured out that you were involved with the CIA in something called the Intersect, she was unstoppable. She started calling the CIA and the NSA. She tried to find me. She even tried to track down Casey. She sent letters. She went to the media. A couple tabloids ran with it, but nothing major."

Sarah smiled. "But she didn't stop there. She called in the big guns. It turns out that her in-laws, Woody and Honey Woodcomb, are rather well connected politically. Pretty soon, Senators Dodd and Lieberman were putting pressure on the DNI to find out what was going on. There were secret hearings in the Senate Intelligence Committee and the House Select Committee on Intelligence regarding the Intersect. Casey, Beckman and I were all called in to testify."

"Yeah, that was fun," Casey grumbled. "Getting my ass chewed by a bunch of senators."

Sarah shot Casey a dirty look and continued. "Finally, Beckman had to admit that she and Graham had ordered an American civilian, you, locked in a bunker without benefit of trial or hearing. The story was leaked to the media. There was a perfect storm of publicity. Ellie was even on Oprah."

Chuck's jaw dropped. He was trying to imagine Ellie on Oprah's couch.

"It was a segment called, 'The Government Kidnapped My Brother.'"

"The CIA and the NSA stalled as long as they could, citing 'National Security.' But it was all too much. You, or rather your situation, was an embarrassment. The howls over Guantanamo were nothing compared to the cries of 'Free Bartowski.' Beckman submitted her resignation yesterday and a Presidential order was signed late last night for your immediate and unconditional release."

"But what about Fulcrum?" Chuck asked. "Aren't I still in danger?"

"Conspiracies operate in secret," Sarah said. "Once word got out, there was a concerted effort to root out Fulcrum from the CIA, the NSA, the FBI, from every government agency. It turns out there was a lot of information on who the Fulcrum agents were, but no one had done a – what do you call it – a full court press to clean it up before. Dozens of Fulcrum operatives have been arrested or fled. They're in complete disarray."

"So I'm finally free?" Chuck asked.

Sarah nodded. "It's over."

"But I still have the Intersect in my head," Chuck said.

Sarah shook her head. "It turns out that Beckman has known for months how to remove the Intersect images from your head. She just didn't want to lose such a valuable asset."

Chuck shook his head. "So where are you taking me now?" he asked.

"The White House," Sarah said. "You're going to receive a personal apology from the President."

"You know," Chuck said. "In all the times you came by, I never asked you who the President was."

"Barak Obama," Sarah said.

"That Senator from Illinois? Not Hillary?"

"No," Sarah said. "Hillary's Secretary of State." Chuck shuddered. "Yeah," Sarah agreed.

"Wow, after all this, it's going to be a little weird going back to the Buy More," Chuck said.

"I, ah, don't think you have to worry about that," Sarah said. "There are dozens of lawyers angling to sue the government on your behalf. And I understand that a couple different publishing companies are already in a bidding war to buy the rights to your story. I think you're going to be a wealthy man, Chuck."

Chuck sat back, stunned. A few hours ago he was a prisoner in an underground government bunker. Now he found out that he was famous and probably rich, too.

"Wow," he said.

"Wow, indeed," Sarah replied.

"What about you?" Chuck asked.

"What about me?" Sarah asked.

"Well, I guess now you'll be off to Jakarta to quell a revolution with a fork."

"No, Chuck. In all the fallout from this, Casey and I were forced to submit our resignations. This is our last mission."

"Oh, Sarah," Chuck said. "I'm sorry."

Sarah smiled shyly. "I'm not," she said.

"You're not?" Chuck asked.

Sarah shook her head. "You know why?"

Chuck shook his head.

Sarah unbuckled her seatbelt and moved over to sit beside Chuck. "Because now it means I can do this," she said. She slipped her hand behind Chuck's head and pulled his lips to hers.

Casey snorted and went up front to see if the pilots needed any help flying the plane.


End file.
